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set_parameters.R
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set_parameters.R
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#' Setting parameters
#'
#' Functionality for altering parameters:
#'
#' @param param_type A character. String specifying type of parameters to make
#' "flat", "prior_mean", "posterior_mean", "prior_draw",
#' "posterior_draw", "define". With param_type set to \code{define} use
#' arguments to be passed to \code{make_priors}; otherwise \code{flat} sets
#' equal probabilities on each nodal type in each parameter set;
#' \code{prior_mean}, \code{prior_draw}, \code{posterior_mean},
#' \code{posterior_draw} take parameters as the means or as draws
#' from the prior or posterior.
#' @param warning Logical. Whether to warn about parameter renormalization.
#' @param ... Options passed onto \code{\link{make_priors}}.
#' @inheritParams CausalQueries_internal_inherit_params
#'
#' @name parameter_setting
NULL
#> NULL
#' Make a 'true' parameter vector
#'
#' A vector of 'true' parameters; possibly drawn from prior or posterior.
#'
#' @rdname parameter_setting
#'
#' @param normalize Logical. If parameter given for a subset of a family the
#' residual elements are normalized so that parameters in param_set sum
#' to 1 and provided params are unaltered.
#'
#' @return A vector of draws from the prior or distribution of parameters
#' @importFrom rstan extract
#' @export
#' @family parameters
#' @examples
#'
#' # make_parameters examples:
#'
#' # Simple examples
#' model <- make_model('X -> Y')
#' data <- make_data(model, n = 2)
#' model <- update_model(model, data)
#' make_parameters(model, parameters = c(.25, .75, 1.25,.25, .25, .25))
#' make_parameters(model, param_type = 'flat')
#' make_parameters(model, param_type = 'prior_draw')
#' make_parameters(model, param_type = 'prior_mean')
#' make_parameters(model, param_type = 'posterior_draw')
#' make_parameters(model, param_type = 'posterior_mean')
#'
#'
#'\donttest{
#'
#' #altering values using \code{alter_at}
#' make_model("X -> Y") %>% make_parameters(parameters = c(0.5,0.25),
#' alter_at = "node == 'Y' & nodal_type %in% c('00','01')")
#'
#' #altering values using \code{param_names}
#' make_model("X -> Y") %>% make_parameters(parameters = c(0.5,0.25),
#' param_names = c("Y.10","Y.01"))
#'
#' #altering values using \code{statement}
#' make_model("X -> Y") %>% make_parameters(parameters = c(0.5),
#' statement = "Y[X=1] > Y[X=0]")
#'
#' #altering values using a combination of other arguments
#' make_model("X -> Y") %>% make_parameters(parameters = c(0.5,0.25),
#' node = "Y", nodal_type = c("00","01"))
#'
#' # Normalize renormalizes values not set so that value set is not renomalized
#' make_parameters(make_model('X -> Y'),
#' statement = 'Y[X=1]>Y[X=0]', parameters = .5)
#' make_parameters(make_model('X -> Y'),
#' statement = 'Y[X=1]>Y[X=0]', parameters = .5,
#' normalize = FALSE)
#'
#' }
make_parameters <- function(model,
parameters = NULL,
param_type = NULL,
warning = TRUE,
normalize = TRUE, ...) {
is_a_model(model)
if (!is.null(parameters) &&
(length(parameters) == length(get_parameters(model)))) {
out <- clean_param_vector(model, parameters)
class(out) <- c("parameters", "numeric")
} else {
if (!is.null(param_type)) {
if (!(
param_type %in% c(
"flat",
"prior_mean",
"posterior_mean",
"prior_draw",
"posterior_draw",
"define"
)
)) {
stop(
paste(
"param_type should be one of `flat`, `prior_mean`,",
"`posterior_mean`, `prior_draw`, `posterior_draw`, or `define`"
)
)
}
}
# Figure out if we need to use make_par_values
par_args <- list(...)
par_args_provided <-
sum(
names(par_args) %in% c(
"distribution",
"alter_at",
"node",
"nodal_type",
"label",
"param_set",
"given",
"statement",
"join_by",
"param_names"
)
)
if (par_args_provided > 0 & is.null(param_type)) {
param_type <- "define"
}
if (is.null(param_type)) {
param_type <- "prior_mean"
}
# New (from parameters)
if (param_type == "define") {
param_value <- make_par_values(model,
alter = "param_value",
x = parameters,
normalize = normalize,
...)
}
# Flat lambda
if (param_type == "flat") {
param_value <- make_priors(model, distribution = "uniform")
}
# Prior mean
if (param_type == "prior_mean") {
param_value <- get_priors(model)
}
# Prior draw
if (param_type == "prior_draw") {
param_value <- make_prior_distribution(model, 1) |> unlist()
}
# Posterior mean
if (param_type == "posterior_mean") {
if (is.null(model$posterior)) {
stop("Posterior distribution required")
}
param_value <- apply(model$posterior_distribution, 2, mean)
}
# Posterior draw
if (param_type == "posterior_draw") {
if (is.null(model$posterior)) {
stop("Posterior distribution required")
}
df <- model$posterior_distribution
param_value <- df[sample(nrow(df), 1),] |> unlist()
}
out <- clean_param_vector(model, param_value)
}
return(out)
}
#' Set parameters
#'
#' Add a true parameter vector to a model. Parameters can be created using
#' arguments passed to \code{\link{make_parameters}} and
#' \code{\link{make_priors}}.
#'
#' @rdname parameter_setting
#'
#' @return An object of class \code{causal_model}. It essentially returns a
#' list containing the elements comprising a model
#' (e.g. 'statement', 'nodal_types' and 'DAG') with true vector of
#' parameters attached to it.
#' @export
#' @family parameters
#' @examples
#'
#' # set_parameters examples:
#'
#' make_model('X->Y') %>% set_parameters(1:6) %>% grab("parameters")
#'
#' # Simple examples
#' model <- make_model('X -> Y')
#' data <- make_data(model, n = 2)
#' model <- update_model(model, data)
#' set_parameters(model, parameters = c(.25, .75, 1.25,.25, .25, .25))
#' set_parameters(model, param_type = 'flat')
#' set_parameters(model, param_type = 'prior_draw')
#' set_parameters(model, param_type = 'prior_mean')
#' set_parameters(model, param_type = 'posterior_draw')
#' set_parameters(model, param_type = 'posterior_mean')
#'
#'
#'\donttest{
#'
#' #altering values using \code{alter_at}
#' make_model("X -> Y") %>% set_parameters(parameters = c(0.5,0.25),
#' alter_at = "node == 'Y' & nodal_type %in% c('00','01')")
#'
#' #altering values using \code{param_names}
#' make_model("X -> Y") %>% set_parameters(parameters = c(0.5,0.25),
#' param_names = c("Y.10","Y.01"))
#'
#' #altering values using \code{statement}
#' make_model("X -> Y") %>% set_parameters(parameters = c(0.5),
#' statement = "Y[X=1] > Y[X=0]")
#'
#' #altering values using a combination of other arguments
#' make_model("X -> Y") %>% set_parameters(parameters = c(0.5,0.25),
#' node = "Y", nodal_type = c("00","01"))
#'
#'
#' }
set_parameters <- function(model,
parameters = NULL,
param_type = NULL,
warning = FALSE, ...) {
# parameters are created unless a vector of full length is provided
if (length(parameters) != length(get_parameters(model))) {
if (!is.null(parameters)) {
parameters <- make_parameters(model,
parameters = parameters,
param_type = "define", ...)
} else {
parameters <- make_parameters(model,
param_type = param_type, ...)
}
}
model$parameters_df$param_value <- parameters
model$parameters_df <- clean_params(model$parameters_df, warning = warning)
return(model)
}
#' Get parameters
#'
#' Extracts parameters as a named vector
#'
#' @rdname parameter_setting
#'
#' @return A vector of draws from the prior or distribution of parameters
#' @importFrom dirmult rdirichlet
#' @family parameters
get_parameters <- function(model, param_type = NULL) {
if (is.null(param_type)) {
x <- model$parameters_df$param_value
names(x) <- model$parameters_df$param_names
class(x) <- c("parameters", "numeric")
}
if (!is.null(param_type)){
x <- make_parameters(model, param_type = param_type)
}
return(x)
}